LAMMPS (21 Nov 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
# Pure HNS crystal, ReaxFF tests for benchmarking LAMMPS
# See README for more info

variable x index 2
variable y index 2
variable z index 2
variable t index 100


units             real
atom_style        charge
atom_modify sort  100 0.0 # optional
dimension         3
boundary          p p p

read_data         data.hns-equil
Reading data file ...
  triclinic box = (0 0 0) to (22.326 11.1412 13.778966) with tilt (0 -5.02603 0)
  2 by 1 by 2 MPI processor grid
  reading atoms ...
  304 atoms
  reading velocities ...
  304 velocities
  read_data CPU = 0.003 seconds
replicate         $x $y $z bbox
replicate         2 $y $z bbox
replicate         2 2 $z bbox
replicate         2 2 2 bbox
Replication is creating a 2x2x2 = 8 times larger system...
  triclinic box = (0 0 0) to (44.652 22.2824 27.557932) with tilt (0 -10.05206 0)
  2 by 1 by 2 MPI processor grid
  bounding box image = (0 -1 -1) to (0 1 1)
  bounding box extra memory = 0.03 MB
  average # of replicas added to proc = 5.00 out of 8 (62.50%)
  2432 atoms
  replicate CPU = 0.000 seconds


pair_style        reaxff NULL
pair_coeff        * * ffield.reax.hns C H O N

compute           reax all pair reaxff

neighbor          1.0 bin
neigh_modify      every 20 delay 0 check no

timestep          0.1

thermo_style      custom step temp pe press evdwl ecoul vol
thermo_modify     norm yes
thermo            10

velocity          all create 300.0 41279 loop geom

fix               1 all nve
fix               2 all qeq/reax 1 0.0 10.0 1e-6 reaxff

run               $t
run               100

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- pair reaxff command: doi:10.1016/j.parco.2011.08.005

@Article{Aktulga12,
 author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
 title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
 journal = {Parallel Computing},
 year =    2012,
 volume =  38,
 number =  {4--5},
 pages =   {245--259}
}

- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005

@Article{Aktulga12,
 author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
 title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
 journal = {Parallel Computing},
 year =    2012,
 volume =  38,
 pages =   {245--259}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Neighbor list info ...
  update: every = 20 steps, delay = 0 steps, check = no
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 11
  ghost atom cutoff = 11
  binsize = 5.5, bins = 10 5 6
  2 neighbor lists, perpetual/occasional/extra = 2 0 0
  (1) pair reaxff, perpetual
      attributes: half, newton off, ghost
      pair build: half/bin/newtoff/ghost
      stencil: full/ghost/bin/3d
      bin: standard
  (2) fix qeq/reax, perpetual, copy from (1)
      attributes: half, newton off
      pair build: copy
      stencil: none
      bin: none
Per MPI rank memory allocation (min/avg/max) = 103.8 | 103.8 | 103.8 Mbytes
   Step          Temp          PotEng         Press          E_vdwl         E_coul         Volume    
         0   300           -113.27833      437.52125     -111.57687     -1.7014647      27418.867    
        10   299.38517     -113.27631      1439.2564     -111.57492     -1.7013814      27418.867    
        20   300.27106     -113.27884      3764.3691     -111.57762     -1.7012246      27418.867    
        30   302.21062     -113.28428      7007.6981     -111.58335     -1.7009363      27418.867    
        40   303.52264     -113.28799      9844.8446     -111.58747     -1.7005186      27418.867    
        50   301.87059     -113.28324      9663.0539     -111.58318     -1.7000523      27418.867    
        60   296.67807     -113.26777      7273.8306     -111.56815     -1.6996136      27418.867    
        70   292.19997     -113.25435      5533.612      -111.55514     -1.6992157      27418.867    
        80   293.58675     -113.25831      5993.4344     -111.55946     -1.6988533      27418.867    
        90   300.62636     -113.27925      7202.8636     -111.58069     -1.6985591      27418.867    
       100   305.38278     -113.29357      10085.719     -111.59518     -1.6983876      27418.867    
Loop time of 6.63333 on 4 procs for 100 steps with 2432 atoms

Performance: 0.130 ns/day, 184.259 hours/ns, 15.075 timesteps/s, 36.663 katom-step/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 4.1006     | 4.5745     | 5.0624     |  17.4 | 68.96
Neigh   | 0.11589    | 0.11637    | 0.11669    |   0.1 |  1.75
Comm    | 0.0077297  | 0.49567    | 0.96958    |  52.7 |  7.47
Output  | 0.00027396 | 0.00031049 | 0.00038633 |   0.0 |  0.00
Modify  | 1.4458     | 1.4461     | 1.4465     |   0.0 | 21.80
Other   |            | 0.0004201  |            |       |  0.01

Nlocal:            608 ave         612 max         604 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost:        5737.25 ave        5744 max        5732 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Neighs:         231539 ave      233090 max      229970 min
Histogram: 1 0 0 0 1 1 0 0 0 1

Total # of neighbors = 926155
Ave neighs/atom = 380.82031
Neighbor list builds = 5
Dangerous builds not checked
Total wall time: 0:00:06
